+Open data
-Basic information
Entry | Database: PDB / ID: 6sm7 | ||||||
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Title | Crystal structure of SLA Reductase YihU from E. Coli | ||||||
Components | 3-sulfolactaldehyde reductase | ||||||
Keywords | OXIDOREDUCTASE / apo / reductase / sulfoquinovose / dihydroxypropanesulfonate | ||||||
Function / homology | Function and homology information sulfolactaldehyde 3-reductase / 4-hydroxybutyrate dehydrogenase / 4-hydroxybutyrate dehydrogenase activity / 3-sulfolactaldehyde reductase activity / 6-sulfoquinovose(1-) catabolic process / 6-sulfoquinovose(1-) catabolic process to glycerone phosphate and 3-sulfolactaldehyde / toxin catabolic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / NADP binding ...sulfolactaldehyde 3-reductase / 4-hydroxybutyrate dehydrogenase / 4-hydroxybutyrate dehydrogenase activity / 3-sulfolactaldehyde reductase activity / 6-sulfoquinovose(1-) catabolic process / 6-sulfoquinovose(1-) catabolic process to glycerone phosphate and 3-sulfolactaldehyde / toxin catabolic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / NADP binding / protein homotetramerization / protein-containing complex / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | ||||||
Authors | Sharma, M. / Davies, G.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Acs Catalysis / Year: 2020 Title: Dynamic Structural Changes Accompany the Production of Dihydroxypropanesulfonate by Sulfolactaldehyde Reductase Authors: Sharma, M. / Abayakoon, P. / Lingford, J.P. / Epa, R. / John, A. / Jin, Y. / Goddard-Borger, E.D. / Davies, G.J. / Williams, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sm7.cif.gz | 232.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sm7.ent.gz | 185.3 KB | Display | PDB format |
PDBx/mmJSON format | 6sm7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sm/6sm7 ftp://data.pdbj.org/pub/pdb/validation_reports/sm/6sm7 | HTTPS FTP |
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-Related structure data
Related structure data | 6smyC 6smzC 2gf2S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: 0
NCS ensembles :
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-Components
#1: Protein | Mass: 32257.246 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: yihU, garR_1, garR_2, garR_3, mmsB, A8C65_00150, AML07_00060, APZ14_22310, AUQ13_20575, AUS26_20040, AW106_21710, BANRA_02548, BANRA_03067, BET08_12475, BHS81_23180, BUE81_09905, BvCms12BK_ ...Gene: yihU, garR_1, garR_2, garR_3, mmsB, A8C65_00150, AML07_00060, APZ14_22310, AUQ13_20575, AUS26_20040, AW106_21710, BANRA_02548, BANRA_03067, BET08_12475, BHS81_23180, BUE81_09905, BvCms12BK_03464, BvCms2454_03851, BvCmsA75A_01696, BvCmsH15A_04687, BvCmsKSP039_00778, BvCmsNSNP006_03738, BvCmsNSNP036_00183, BvCmsOUP014_01268, BvCmsSINP012_03704, BvCmsSINP036_03005, BvCmsSIP019_01210, BvCmsSIP044_01085, C2U48_13500, C4J69_10130, C5N07_19050, C5P01_22840, CA593_06580, COD30_17900, CV83915_02180, D0X26_17330, D3821_15280, D9I97_17995, D9J11_11940, DIV22_13840, DL800_27080, DNQ41_00720, E2855_04886, E2863_04195, E4Z89_22515, EAI42_02715, EAI52_23825, EC1094V2_4430, EC3234A_72c00280, EC3426_00187, EC95NR1_03333, ED600_18125, EEP23_19010, EKI52_16085, EL75_4302, EL79_4554, EL80_4461, EPS71_08590, EPS97_11270, ERS150876_03348, EXX32_12725, EYD11_22365, FORC28_5901, NCTC10090_02897, NCTC10865_06042, NCTC13462_03726, NCTC8500_05456, NCTC8960_02460, NCTC9037_04932, NCTC9045_05673, NCTC9058_02032, NCTC9062_03294, NCTC9706_02118, RK56_017955, SAMEA3484427_03349, SAMEA3484429_03464, SAMEA3752557_02792, SAMEA3752559_05062, SAMEA3753300_04042, WQ89_24850 Production host: Escherichia coli (E. coli) References: UniProt: A0A066Q5Q8, UniProt: P0A9V8*PLUS, sulfolactaldehyde 3-reductase #2: Chemical | ChemComp-BO3 / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium Malonate dibasic, Imidazole, Boric acid (MIB) buffer, 25% w/v PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9772 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9772 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→56.89 Å / Num. obs: 96966 / % possible obs: 100 % / Redundancy: 8.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.024 / Rrim(I) all: 0.068 / Net I/σ(I): 17.7 / Num. measured all: 781985 / Scaling rejects: 355 |
Reflection shell | Resolution: 1.88→1.91 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.848 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4763 / CC1/2: 0.623 / Rpim(I) all: 0.315 / Rrim(I) all: 0.906 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GF2 Resolution: 1.88→56.81 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.107 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.4 Å2 / Biso mean: 30.194 Å2 / Biso min: 19.06 Å2
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Refinement step | Cycle: final / Resolution: 1.88→56.81 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 1.88→1.929 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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